I tried all of your tips, but no one works. I must missed something. I tried removed
- org.eclipse.ui.navigator.viewer
- org.eclipse.ui.navigator.navigatorContent
- org.eclipse.ui.navigator.linkHelper
from extensions nothing.

I comment and then delete the extension points from plugin.xml and nothing.

This should really disable drag and drop function in project explorer window of running application? But thx for previous advice.

weired, because if you disable the navigator-content, the projectexplorer shouldn't display any children of your diagram and model files at all. So, I don't really know how you could drag/drop.

Please make sure to test your plugins in a clean runtime-application. Maybe there are still some "old" deployed plugins, that get activated.

Another thing that came to my mind:
if you just want to disable the drag and drop (generated for shortcuts by gmf as default), you could also remove the following entries in your gmfgen for the Gen Diagram XXXEditPart:
- Diagram
-> Contains Shortcuts To
-> Contains Shortcuts Provided For
and regenerate the code.
This should preserve the display of the content, but disable default drag and drop as shortcuts.
So you could leave the generated navigator stuff in place in this case.